support of medium modification and cobra model loading

[hariszaf]

Aim of this PR is to address issues #74 and #75 .

The MetabolicNetwork class has been modified now it keeps the exchange reactions of a model as model.exchanges and its medium as model.medium.

The user may modify the medium as in cobra.

On top of that, dingo can also now build a dingo-model based on a cobra-model.
For example:

import cobra 
import dingo 

cobra_model = cobra.io.read_sbml_model("my_model.xml")
dingo_model = dingo.MetabolicNetwork.from_cobra_model(cobra_model)

This allows for further modifications of the model, e.g. adding reactions, through the
convenient interface of cobra and an easier integration with dingo.

[TolisChal]

Hey, @hariszaf, thanks a lot for this PR!

Could you plz add one unit-test per new function to check for correctness?
e.g., load a model that you know the medium and inter-medium reactions and check if the new functions find them correctly.

[hariszaf]

@TolisChal here's a test for editing a reaction that is already part of the medium.
The user will be able to edit the medium with reactions that are included in the model.exchanges list.
If they need to add a new reaction, then it would be better to do so using cobra and once they have the model as they want, the can use the dingo.MetabolicNetwork.from_cobra_model().
That's probably something that we should add on the tutorial too.

[TolisChal]

How this can be true if model.lb[glc_index] != -1.5?

[TolisChal]

Does this test that the medium are extracted correctly?
How many medium reaction does ecoli has?
I was thinking something like:
known_medium = {"medium_reaction1": medium_reaction1_index, .... }
and then check if the extracted medium reactions and its indices matches with the already known medium reactions and indices

[hariszaf]

Do you mean something like that?
The check for the number of exchange reactions is in case in the future we enable to add an exchange reaction, rather than just editing its boundaries.

[TolisChal]

Yes, exactly. Thanks!